Align Inner-membrane translocator (characterized, see rationale)
to candidate HSERO_RS05325 HSERO_RS05325 ribose ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__HerbieS:HSERO_RS05325 Length = 328 Score = 159 bits (402), Expect = 9e-44 Identities = 100/304 (32%), Positives = 169/304 (55%), Gaps = 7/304 (2%) Query: 8 PLWITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVG 67 PL + + L+ + L+ D F + N+LR + + I A+GM+ VI++GGIDLSVG Sbjct: 28 PLALPLAGLVVVSLLMGLASDNFFTLSNWFNVLRQVSIVGILAVGMSFVILTGGIDLSVG 87 Query: 68 AVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFL 127 A +AL+G +++ LI LA + + L T G L G ++ ++ IVTLA M + Sbjct: 88 AAMALAGTISAGLIVNSGLPAPLALLCGVGLATCIGLLNGALVAWGRMPAIIVTLATMGV 147 Query: 128 ARGLATTLSEESIAIDHPFYDAVAEMSIALPGN-GALDLSSLIFILFFVIIAVVMHYTRF 186 ARG+ S +P +S G G + + ++ ++ + + +++ T F Sbjct: 148 ARGVGLIYSG-----GYPISGLPGWISWFGVGRIGMVPVPVILMLIVYALAWLLLQRTAF 202 Query: 187 GTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVEL 246 G +VYAIGGN+ +A L G+ + +++YAIS F + LA I+ T SG +G EL Sbjct: 203 GRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGFEL 262 Query: 247 DAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFI 306 DAIAAVV+GGT + GG G V+GT++G +L+G++ + G ++ + I+ G+++ I Sbjct: 263 DAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLNLMG-INPYLQDIIRGVIILLAI 321 Query: 307 LLQK 310 + + Sbjct: 322 YIAR 325 Lambda K H 0.330 0.145 0.424 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 379 Number of extensions: 24 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 320 Length of database: 328 Length adjustment: 28 Effective length of query: 292 Effective length of database: 300 Effective search space: 87600 Effective search space used: 87600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory